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A Python library for Atom Probe Tomography analysis

Project description

APAV: Python analysis for atom probe tomography

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APAV (Atom Probe Analysis and Visualization) is a Python library for the analysis and visualization of atom probe tomography experiments.

  • Multiple event dependent mass or time-of-flight spectra
  • Correlation histograms
  • Molecular isotopic calculations
  • .pos, .epos, .ato files or synthetic data
  • Mass spectrum quantification with multiple fitting schemes
  • Interactive visualizations

APAV can perform a number of analyses common in field evaporation science, although it focuses on analyses relating to detector multiple events. A "Multiple event" refers to a phenomenon where multiple ions (elemental or molecular) strike the micro-channel plates between pulses.

APAV is open source (GPLv2_ or greater) and runs on Windows, Linux, Mac OS - or anything able to run a python interpreter. It is written in Python 3 using NumPy to accelerate mathematical computations, and other math tools for more niche calculations. Visualizations leverage pyqtgraph and other custom Qt widgets.


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Documentation is found at:


Why use this over IVAS or program X?

APAV was never intended to be used as an IVAS substitute or replacement. While much of the functionality may be similar/redundant, APAV fills feature gaps in IVAS found lacking (or simply non-existent). Specifically:

  1. Multiple-event analysis (correlation histograms, multiple event histograms, multiple event mass quantifications.
  2. Full control over mass spectrum analysis (background models, fitting, binning).
  3. Provide an interface for developing custom analyses through common ePOS, POS, ATO, RNG, RRNG files.

Why is there no GUI for APAV?

As APAV is a python library, there is no plan for a graphical user interface for APAV. It does, however, include custom interactive visualization tools using pyqtgraph and custom Qt widgets (for various graphing).

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